Eva-Maria Gerlach

1.6 Mb deletion in chromosome band 3q29 associated with eye abnormalities

We report on a patient with a de novo microdeletion 3q29 detected by molecular karyotyping using array CGH analysis. The girl displayed microphthalmia and cataract, hyperplastic pyloric stenosis, mild dysmorphic facial features, and developmental delay. Array CGH analysis uncovered a 1.6Mb deletion within chromosome band 3q29, which overlaps with the commonly deleted region in 3q29 microdeletion syndrome. According to published data, none of the patients with deletion 3q29 showed either congenital cataract and microphthalmia, or other ocular features. Our report expands the phenotypic spectrum of the 3q29 microdeletion syndrome by adding structural eye malformations.

Novel CIC point mutations and an exon-spanning, homozygous deletion identified in oligodendroglial tumors by a comprehensive genomic approach including transcriptome sequencing.

Oligodendroglial tumors form a distinct subgroup of gliomas, characterized by a better response to treatment and prolonged overall survival. Most oligodendrogliomas and also some oligoastrocytomas are characterized by a unique and typical unbalanced translocation, der(1,19), resulting in a 1p/19q co-deletion. Candidate tumor suppressor genes targeted by these losses, CIC on 19q13.2 and FUBP1 on 1p31.1, were only recently discovered. We analyzed 17 oligodendrogliomas and oligoastrocytomas by applying a comprehensive approach consisting of RNA expression analysis, DNA sequencing of CIC, FUBP1, IDH1/2, and array CGH. We confirmed three different genetic subtypes in our samples: i) the “oligodendroglial” subtype with 1p/19q co-deletion in twelve out of 17 tumors; ii) the “astrocytic” subtype in three tumors; iii) the “other” subtype in two tumors. All twelve tumors with the 1p/19q co-deletion carried the most common IDH1 R132H mutation. In seven of these tumors, we found protein-disrupting point mutations in the remaining allele of CIC, four of which are novel. One of these tumors also had a deleterious mutation in FUBP1. Only by integrating RNA expression and array CGH data, were we able to discover an exon-spanning homozygous microdeletion within the remaining allele of CIC in an additional tumor with 1p/19q co-deletion. Therefore we propose that the mutation rate might be underestimated when looking at sequence variants alone. In conclusion, the high frequency and the spectrum of CIC mutations in our 1p/19q-codeleted tumor cohort support the hypothesis that CIC acts as a tumor suppressor in these tumors, whereas FUBP1 might play only a minor role.

Severe intellectual disability, West syndrome, Dandy–Walker malformation, and syndactyly in a patient with partial tetrasomy 17q25.3

We report on a de novo 0.5 Mb triplication (partial tetrasomy) of chromosome 17q25.3 in a 10‐year‐old girl with severe intellectual disability, infantile seizures (West syndrome), moderate hearing loss, Dandy–Walker malformation, microcephaly, craniofacial dysmorphism, striking cutaneous syndactyly (hands 3–4, feet 2–3), joint laxity, and short stature. The triplication resulted from the unusual combination of a terminal duplication at 17qter and a cryptic translocation of an extra copy of the same segment onto chromosome 10qter. The breakpoint at 17q25.3 was located within the FOXK2 gene. SNP chip analysis suggested that the rearrangement occurred during paternal meiosis involving both paternal chromosomes 17.

Partial deletion of GLRB and GRIA2 in a patient with intellectual disability.

We report about the partial de novo loss of GLRB and GRIA2 in an individual with intellectual disability (ID). No additional mutations were found in either gene. GLRB itself does not seem to be a good candidate as it causes autosomal recessive hyperekplexia and no symptoms were found in the patient. Mutations of GRIA2 have not been described as cause of ID to date. Nonetheless, it is a very attractive candidate because it encodes a subunit of a glutamate receptor, which is highly expressed in postsynaptic structures and has an important role in signal transduction across synapses. Although we were able to isolate a fragment of a fusion transcript of both genes from the patients blood, we were not able to isolate a transcript with an open reading frame throughout the entire length. The reading frame could be restored by differential splicing, which might take place in brain tissue but not in blood. We assume that either haploinsufficiency of GRIA2 or a GLRB/GRIA2 fusion gene leading to a protein with dominant-negative properties is causing the phenotype of the patient.

Abstract 3415: Genetic analysis of multifocal glioblastoma multiforme foci points to their monoclonal evolution and highlights early and late events in their development

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Glioblastoma (GBM) is the most common and malignant type of brain tumor in adults with an average survival time of less than a year. A hallmark of GBM is its infiltrating growth hampering successful surgical treatment and precluding curative therapy. Multifocal GBMs - multiple synchronous lesions in the same patient - represent approximately 8-10% of all gliomas and generally have a poor prognosis. There are two theories as to the nature of these multifocal GBMs: they could either have originated from one main GBM or they can be independent tumors. Genetic studies of multifocal GBMs are very rare and such studies could elucidate the nature of these tumors. We have analyzed eleven tumor foci of six patients with multifocal GBMs using array comparative genome hybridization (aCGH), spectral karyotyping (SKY), and Sanger sequencing of PTEN, TP53, and IDH1/2. Array CGH analysis of ten of the tumors revealed multiple genetic aberrations. The most frequent were gain of chromosome 7 (9/10), amplification of EGFR (10/10), loss of chromosome 10 (10/10), and partial loss of chromosome 9 (7/10). SKY analysis identified multiple translocations including complex rearrangements. None of the tumors carried a mutation in IDH1/2 and they were genetically similar to primary GBMs although they exhibited unique characteristics; e.g. all carried an EGFR amplification, indicating that it is important for the multifocal phenotype. Tumor foci derived from the same patient always shared identical aberrations, proving monoclonal origin of these tumors but also exhibited additional aberrations, which were specific for each focus and therefore must have occurred later in tumor development. Moreover, our results show that events important for gliomagenesis could occur at different time points in tumor evolution: for example, the region involved in the EGFR amplification was different in both foci from three patients and identical in two foci from one patient. The same can be said of point mutations in TP53 and PTEN; TP53 mutations were identical in the different foci from one patient and different in another patient while PTEN mutations were different in the foci from two patients and similar in those of one. Interestingly, in each patient one focus always contained more aberrations than the other, highlighting the possibility that one derived from the other; this would further support the hypothesis that multifocal GBMs are of monoclonal origin and then develop independently of each other by clonal evolution. Taken together, multifocal GBM provide an excellent model for investigating tumor progression and invasion and might help to distinguish between driver and passenger alterations in GBM. Acknowledgements: This work was partially supported by a grant (MeDDrive program) of the Medizinische Fakultat Carl Gustav Carus, Technische Universitat Dresden. Citation Format: Khalil Abou-El-Ardat, Dietmar Krex, Michael Seifert, Kerstin Becker, Morten Hillmer, Sophie Eisenreich, Arleta Kasner-Frensel, Petra Freitag, Eva-Maria Gerlach, Karl Hackmann, Andreas Rump, Gabriele Schackert, Evelin Schrock, Barbara Klink. Genetic analysis of multifocal glioblastoma multiforme foci points to their monoclonal evolution and highlights early and late events in their development. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3415. doi:10.1158/1538-7445.AM2014-3415

Abstract 3387: Upregulation of gene expression in oligodendrogliomas is linked to an increase in GA binding protein alpha transcription

Lower grade gliomas can be histologically classified into astrocytomas, oligoastrocytomas, or oligodendrogliomas. The latter have come into focus because of their interesting characteristics: they have a more favorable outcome and better response to chemo/radiotherapy. This is correlated with a unique unbalanced translocation der(1;19)(q10;p10) causing a codeletion of the short arm of chromosome 1 and the long arm of chromosome 19. Like the other lower grade gliomas, a large percentage of oligodendrogliomas carry the IDH1 R132 mutation and this is associated with the presence of the codeletion. We identified a high number of mutations in the remaining alleles of the Capicua homolog gene (CIC) and in the far upstream element binding protein (FUBP1) in 1p/19q codeleted oligodendrogliomas (Eisenreich et al. 2013, doi:10.1371/journal.pone.0076623). Both genes are suspected to act as tumor suppressor genes. We then analyzed the expression profiles of 13 oligodendrogliomas and oligoastrocytomas both with the 1p/19q codeletion (nine samples) and without (four samples) using a combination of expression microarrays and transcriptome sequencing (RNA-Seq). Our results showed that all nine samples with the 1p/19q codeletion carried the heterozygous IDH1 R132H mutation while only one tumor without the codeletion carried said mutation. There was a high concordance between the results of RNA-Seq and the microarray experiments and both showed a distinctive expression signature between samples with the 1p/19q codeletion and those without. Using MSigDB, we found that the genes whose expression was altered in in tumors with the 1p/19q codeletion showed significant overlap with those involved in stemness and differentiation and genes that had CpG-rich promoters. Furthermore, there was an overlap with genes with altered expression in chronic myelogenous leukemia (CML). When we compared the expression of genes located on 1p and 19q between the tumors with the 1p/19q codeletion and those without, we found that only 82% of genes on 1p and 19q were downregulated significantly. When we ran the upregulated genes in PathScan, we found enrichment in GA binding protein alpha (GABPA)binding sites. GABPA expression levels were increased in our glioma samples with and without the 1p/19q codeletion. Investigating the expression levels of GABPA in the Cancer Genome Atlas (TCGA) GBM dataset also revealed an upregulation of this transcription factor. An increase in GABPA-mediated transcription was recently reported in CML but has not been yet reported in gliomas. We therefore propose that GABPA is an important transcription factor in gliomas. We are currently evaluating the function of GABPA in glioma what will also be presented. Acknowledgements: This project was partially supported by a MeDDrive grant of the Medizinische Fakultat Carl Gustav Carus, Technische Universitat Dresden. Citation Format: Barbara Klink, Karol Szafranski, Jaime Campos-Valenzuela, Sophie Eisenreich, Dietmar Krex, Eva-Maria Gerlach, Karl Hackmann, Andreas Rump, Gabriele Schackert, Matthias Platzer, Lars Kaderali, Evelin Schrock, Khalil Abou-El-Ardat. Upregulation of gene expression in oligodendrogliomas is linked to an increase in GA binding protein alpha transcription. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3387. doi:10.1158/1538-7445.AM2014-3387

A new autosomal dominant syndrome of distinctive face showing ptosis and prominent eyes associated with cleft palate, ear anomalies, and learning disability.

We report on three patients from two families with apparently a novel clinical entity. The main features of which include unusual craniofacial dysmorphism with ptosis, prominent eyes, flat midface, Cupids bow configuration of the upper lip, low‐set, posteriorly rotated small ears, as well as conductive hearing loss, cleft palate, heart defect, and mild developmental delay. We suggest that this entity is an autosomal dominant disorder given the occurrence in a mother and daughter as well as in an unrelated boy.

Abstract 782: Characterization of genetic changes in oligodendroglial tumors including glioblastomas with oligodendroglial component

In contrast to astrocytic tumors including glioblastomas (GBM), oligodendrogliomas (O) show a better prognosis and increased responsiveness to chemotherapy. Interestingly, a small subgroup of glioblastomas contains areas with histological features of oligodendroglial differentiation. In the current WHO classification (2007) these tumors are now included as a variant of glioblastomas and are called glioblastomas with oligodendroglial component (GBMO). However, definitive diagnostic criteria still do not exist. In this study we used a genome wide approach (chromosomal comparative genomic hybridization (CGH) and molecular karyotyping) in combination with interphase fluoreszence in situ hybridization (FISH) (regions 1p, 1q, 7q, 10q, 17p, 19q, cen18, 21q) to genetically characterize GBMO and “classical” O. We analyzed the oligodendroglial and the astrocytic glioblastoma parts of 13 GBMO separately by chromosomal CGH of microdissected paraffin embedded tumor tissue and interphase FISH on paraffin sections. Furthermore, freshly frozen material of six oligodendrogliomas (4 WHO grade II, 6 WHO-grade III) was examined genome wide by using the standard Agilent 244A chip. We identified four distinct genetic subtypes in GBMO: an “astrocytic” subtype (9/13) characterized by +7/-10; an “oligodendroglial” subtype with −1p/-19q (1/13); an “intermediate” subtype showing +7/-1p (1/13), and an “other” subtype having none of the former aberrations typical for gliomas (2/13). In contrast, most “classical” O (5/6) showed combined 1p/19q deletion, corresponding genetically to the “oligodendroglial” subtype. Four of the O with 1p/19q codeletion showed additional aberrations (e. g. −4, −14, −9, −18). The different histological tumor parts of GBMO revealed common genetic changes in all tumors and showed additional aberrations specific for their oligodendroglial and astrocytic parts. These findings demonstrate the monoclonal origin of the tumor followed by the formation of the astrocytic and oligodendroglial components. We are currently evaluating the array CGH results of six oligodendrogliomas, which will also be presented. The diagnostic determination of these genetic signatures may allow for a better prognostication of the patients. Our results underline the importance of molecular cytogenetic analyses to supplement the histological diagnosis of gliomas. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 782.